plotRarefactionCurve: Plot rarefaction and extrapolation curves for samples

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Plot rarefaction and extrapolation curves for samples

Description

Given a study table, for each sample plot rarefaction curves to estimate repertoire diversity. The method used to generate the rarefaction curve is derived from Chao et al., (2014) using the iNEXT library

Usage

plotRarefactionCurve(study_table)

Arguments

study_table

A tibble consisting antigen receptor sequencing data imported by the LymphoSeq2 function readImmunoSeq(). "junction_aa", "duplicate_count", and "duplicate_frequency" are required columns.

See Also

runINext()

Examples

file_path <- system.file("extdata", "TCRB_sequencing",
 package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
LymphoSeq2::plotRarefactionCurve(study_table)

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.